Inexpensive gene copier for DIY molecular biology

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At a recent O'Reilly/Nature/Google Science Foo Camp, a group of smart folks interested in DIY biology discussed how DNA tests for infectious diseases and the potential of molecular biology in general was unlikely to make it to developing nations anytime soon. The essential tool, a PCR machine that makes copies of DNA fragments, is just too damn expensive. So rather than shrug and move on, they decided to put their ingenuity where their mouths are and make a small, inexpensive PCR machine. The LavaAmp, a portable device for cheap PCR in the field and DIY biotech, is now in prototype. From an email written by Venezuelan biologist Guido Núñez-Mujica, co-developer of the LavaAmp:

LavaAmp is the result of the collaboration of Rob Carlson and his
engineering partner, Rik Wehbring, founders of Biodesic, a Bioengineering firm, Jim Hardy,
bioentrepreneur founder of Gahaga Biosciences, Joseph Jackson, a
philosopher interested in Open Science and DIY Biology and me, a comp.
biologist. SciFoo put us in touch, and in my particular case, exposed
me to a culture of entrepreneurship that I was not familiar with. It
was the catalyst that made us embark in this venture: Try to develop,
manufacture and market a simple, inexpensive device to perform PCR,
the backbone of molecular biology, based on existing technology that
was never developed until we took it over.

Right now, we have developed a prototype and are about to start the manufacturing, if we can get enough funds. In order to gather funds we are competing in a program for social entrepreneurs, The Unreasonable Institute, where we need pledges from supporters in order to gain access
to training, mentoring and funding.

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Ok so back in the day in Africa people used to do PCR by taking three ordinary hot plates and putting a glass bowl on top of each one and use a thermometer to get the temperature of each water bath correct. Then they paid some poor to use a stopwatch and hold a PCR tube in one bath for say 30 seconds, then move the tubes to the second bath for 15, and then into the third for thirty seconds…repeat however many number of cycles you needed…still the cheapest PCR machine to date

As #8 noted, thermocyclers are expensive because the price usually includes a licence to do PCR; cheap thermocyclers will result in lawsuits.

That said, thermocyclers are also used for a variety of things that require much more rigorous control than just basic PCR needs. Certainly, you can do basic PCR with water baths if you don’t need to worry about patents. You won’t have a heated lid, however, so you’ll need to worry about evaporation within the tubes, or use annoying oil techniques. And you’ll need to constantly monitor the temperature if you’re doing something sensitive: for some of my uses of thermocyclers, I need tubes to stay within around 0.2C for several days, and for some others, I need the tubes to have their temperatures varied very carefully.

It’s also worth noting that, as far as lab equipment goes, thermocyclers are rather cheap. Even a modern thermocycler on the used market often sells for around $1k-$2k, and older cyclers that are more annoying to use often sell for a few hundred, assuming one can’t find a lab that will pay you to dispose of them.

BCarver: Beyond a simple non-defrosting freezer, I don’t think much else is really needed for refrigeration for basic PCR reagents.

BCarver1: PCR can be quite cheap per reaction, less than 50 cents (http://www.nervenet.org/papers/pcr.html), and there are some polymerases that can be dried and stored at room temperature. The limiting cost of PCR in countries like Venezuela is indeed the thermal cycler.

Anon #5: Yes, a 3 bath setting is cheap, but cumbersome and time consuming, prone to errors. LavaAmp can perform amplification in less than 30 min.

yer_maw #7:
The architecture is completely different, LavaAmp is not based on a Peltier block, but on convection.

Anon #8: AFAIK, the original patents are expired since at least 4 years,and this is a very different device.

Chevan #9: Primers are already fairly cheap, agarose gels are not the only option to detect DNA and there are many people working on making biology more accessible (easier, cheaper) to regular people. This project is only one among many, from cheaper gel boxes (www.pearlbiotech.com/) to home made culture media (http://letters.cunningprojects.com/?p=97). There are several non-hazardous dyes for DNA too. They pass the Ames test.

WA #10: I would like to know more about the licenses, so far, I have seen that the patent expired a long time ago. If I am wrong, I would like to know more about it.
And, sadly 2K is still too much for a school on a hospital in Venezuela, which is in bad shape, but not even close to poorer countries. This device should be a whole order of magnitude less than current prices, and portable.

With regard to #2, Guido is a Finalist in the Unreasonable Institute [http://is.gd/9Bk2q], so perhaps you would consider micro-funding him for this, which can lead to as much as $150K in funding (more than enough for us to get started). Other than that, we have enough money to be self funded but are still soliciting funding from a variety of sources.

for #4, we estimate the consumable cost per reaction would be less than $5 and we’re working on room temperature stable (and even ambient and remote/extreme temp) substrates.

As noted elsewhere, the Roche license requirement for PCR expired 4 yrs ago so no need to worry about that, although there are a number of patents related to buoyancy-driven PCR we need to pay attention to. Suffice to say, we have it covered.

Our big challenge is going to be detection, because even if you can run PCR remotely, it doesn’t do you much good if you need to whip out a power supply and gel box for detection. We have some ideas employing dipstick format, or even simple DNA sensors, but this will likely not be ready for another 2 years.

Hope to have first commercial units for sale by 4Q 2010 or 1Q 2011.

And for #6, you need to have a science-nerdy sort of chick (or guy) who is turned on by PCR. Not working so well on my wife…

I am one of the developers of the LavaAmp hardware Guido is holding. That hardware is powered off a USB connection, which could be from a netbook. We have plenty of headroom on the power budget and microprocessor for real-time detection, though that will probably wait for a further design revision.

Re the cost — I would say that PCR instruments are expensive not because they have to be, but because they can be. As noted above, the original patents on PCR have either expired or been limited through court rulings. Existing PCR patents cover specific instruments, improved enzymes, or other tidbits that you can pay for but don’t actually need to make anything work. Buying improved enzymes includes a license anyway, and I have never seen a restriction that you could only use a given razor blade in a particular razor. So I don’t see that this will be a problem for us, but I suppose I could be surprised. In any event,as Guido and Jim note, the LavaAmp uses convection PCR, which is covered by a different set of patents that are either expired or that we already have a license for. Conversations with reagent suppliers lead me to believe that the patent situation on real-time detection in this format is so messed up that nobody thinks any protection is possible.

Awesome work here. This really gets me going for not only the future of under-developed countries but also for home dna testing usage. Any idea how one of these bargain priced hand-held thermocyclers would match up against an industrial pcr thermal cycler, such as these : http://thermalcycler.net/ ?